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Quantitative proteomics using uniform 15N-labeling, mascot and the trans-proteomic pipeline

Palmblad, M. , Bindschedler, L.V. and Cramer, R. (2007) Quantitative proteomics using uniform 15N-labeling, mascot and the trans-proteomic pipeline. Proteomics, 7 (19). ISSN 1615-9853

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To link to this item DOI: 10.1002/pmic.200700180


Stable isotope labeling combined with MS is a powerful method for measuring relative protein abundances, for instance, by differential metabolic labeling of some or all amino acids with 14N and 15N in cell culture or hydroponic media. These and most other types of quantitative proteomics experiments using high-throughput technologies, such as LC-MS/MS, generate large amounts of raw MS data. This data needs to be processed efficiently and automatically, from the mass spectrometer to statistically evaluated protein identifications and abundance ratios. This paper describes in detail an approach to the automated analysis of uniformly 14N/15N-labeled proteins using MASCOT peptide identification in conjunction with the trans-proteomic pipeline (TPP) and a few scripts to integrate the analysis workflow. Two large proteomic datasets from uniformly labeled Arabidopsis thaliana were used to illustrate the analysis pipeline. The pipeline can be fully automated and uses only common or freely available software.

Item Type:Article
Divisions:Life Sciences > School of Biological Sciences
ID Code:10064
Uncontrolled Keywords:Arabidopsis , Bioinformatics , Liquid chromatography-tandem mass spectrometry , Quantitative analysis

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